Update the new feature for 4.7

[nroduit]

Changes since v4.6.6 → next release v4.7.0

🆕 New Features

OpenGL 3.3 Volume Rendering Backend (macOS support) — #784

• Added a new FBO (Framebuffer Object) + Fragment Shader rendering pipeline using OpenGL 3.3 core profile.
• This enables Volume Rendering on macOS (previously blocked by deprecated OpenGL APIs).
• Introduced weighted-splatting accumulators and improved FBO texture sizing.
• The Volume class is now used as the primary input for all 3D rendering (MPR/MIP and VR).

Hanging Protocols — Part I

• Changed the view container layout to lay the groundwork for Hanging Protocol support.
• This is the first step toward configurable automated layout of series on screen.

Unified DICOM Import UX — #793

• DICOM-ZIP files can now be drag-and-dropped directly into Weasis.
• All local DICOM import methods (folder, file, ZIP) have been consolidated into a single "Local Device" dialog for a more consistent user experience. So DICOM-ZIP can be imported via the same dialog as folders/files.

Export Annotation Feature (finalized)

• The export of graphical annotations to external formats has been fully implemented and finalized.

4D Series Sub-Series Splitting Dialog — #763

• A dialog to automatically divide a multi-phase 4D series into individual phase sub-series (usable in MPR, MIP, and VR).

Integrated MIP Projection Mode in Standard 2D Viewer — #795

• MIP projection mode is now available directly in the standard 2D viewer with full synchronization and slab geometry overlay.

DICOM Export for MPR Views — #796

• Added the ability to export MPR views as DICOM files with the current orientation.

MPR Crosshair Cut Mode for 3D Volume Rendering — #799

• Introduced a crosshair cut mode that allows interactive slicing/clipping of 3D volume rendering from MPR crosshair positions.

Expanded DICOM Segmentation Support (BINARY, FRACTIONAL, LABELMAP) with MPR & 3D overlay

• DICOM SEG reader now supports the three (0062,0001) SegmentationType kinds defined by the standard:
  • BINARY (already supported, refactored),
  • FRACTIONAL (PROBABILITY and OCCUPANCY) — rendered through a new FractionalOverlay with per-segment alpha LUT (ByteLutAlpha),
  • LABELMAP — single frame per slice where the pixel value is the SegmentNumber, decoded via the new LabelMapContourLoader / LabelMapScanner.
• Segmentation overlays are now displayed not only in the 2D viewer but also in MPR (axial/coronal/sagittal/oblique) and 3D Volume Rendering views. A new SegmentationVolume / SegmentationVolumeBuilder pipeline reslices SEG masks into the active reference volume so the overlay follows the MPR planes and the VR camera.
• New SegVolumeTexture exposes the segmentation volume as an OpenGL texture consumed by the volume shader (vrFunctions.glsl, volumeFbo.frag, voxelUniforms*.glsl).
• The RT module (RTDose) now reuses the same fractional overlay infrastructure for isodose rendering — see commit 426477213 ("Refactoring RT module and use fractional overlay for RTDose").
• Reorganized DICOM codec: SEG-related classes moved into a dedicated org.weasis.dicom.codec.seg package, with HiddenSeriesManager to track non-displayable series referenced by SEG/RT objects.

System File Chooser — #761

• Weasis now uses the system native file chooser instead of the Java common one, providing a more familiar file browsing experience on each platform.

Customizable Keyboard Shortcuts — #804 (uncommitted)

• Added a centralized ShortcutManager to manage all keyboard shortcuts in the application.
• New Shortcuts preferences panel (ShortcutPrefView) allowing users to view, search, customize, and reset keyboard shortcuts.
• Supports conflict detection, per-user persistence, and export/import of shortcut configurations.

Tab Opening Preferences for Studies — #806

• Redesigned the tab opening preferences for studies to improve usability and handle different import contexts (e.g., new study vs. same study, local vs. network).
• Introduced TabFocusPolicy for configurable focus behavior when opening new viewer tabs.

View Synchronization Overhaul — auto-sync, manual-sync, per-view configuration

A complete redesign of how synchronization is controlled, both globally and per view. Documented in the View Synchronization tutorial.

• Per-view auto-sync overlay button {{< icon synch >}} on every eligible 2D view (bottom-right corner). Red = OFF, green = ON. Clicking it opens a per-view popup with:
  • a master Synchronize this view toggle,
  • independent per-action checkboxes for Scroll, Pan, Zoom, Rotation, Flip, Window/Level and Spatial unit (stay-open while you flip several),
  • Apply to all synchronized views — propagates this view's settings to every other view in the same FoR group,
  • an explicit Close item.
• FoR color chip — a small colored square painted at the center of the auto-sync button when the container holds two or more views with different Frame of Reference UIDs. Same UID ⇒ same color (deterministic palette of Kelly's 22-color contrast set, red/white removed), so spatial groupings are visible at a glance. The chip is reused as the icon on every Apply to all synchronized views menu entry to identify the source group.
• Per-view manual-sync overlay button (hand icon) for views that have no — or a different — FoR than their peers. Eligibility requires the same orientation. A click auto-joins an existing manual group, auto-links when there is a single candidate, or shows a multi-select picker when there are several. Once active, Scroll propagation is forced on and locked; other per-action toggles remain freely configurable.
• MPR "Synchronize" submenu added to the per-view configuration popup (settings icon, top-right of each MPR view). Same content as the per-view 2D popup minus the master toggle (synchronization between MPR planes is structural).
• Toolbar drop-down popup overhaul — the synchronization {{< icon synch >}} drop-down now also exposes the per-action checkboxes (mirroring the selected view) and an Apply to all views entry decorated with the selected view's FoR chip.
• None synchronization mode removed — the toolbar drop-down now lists only Default Stack and Default Tile. Use the master Synchronize checkbox in the drop-down popup to disable synchronization globally for the container.
• Revised Default Stack defaults — only Scroll is propagated by default; every other per-action toggle (Pan, Zoom, W/L, Rotation, Flip, Spatial unit) starts disabled and the user opts in explicitly. Previously W/L and Zoom were also on by default. Default Tile is unchanged: every per-action setting still propagates so a tile group stays in lock-step.

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🔧 Improvements

3D / Volume Rendering

• Volume class overhauled: better min/max handling in subclasses, validation of parallel and regular slices, support for color images (byte & short), ability to read and save 3D raw data.
• Improved volume array structure and integration into the rendering pipeline.
• Improved FBO texture size management.

MPR (Multi-Planar Reconstruction)

• Fixed horizontal banding/striations in coronal/sagittal MPR views — #771
• Fixed deformed axial images in non-axially scanned volumes — #752
• Fixed MPR geometry computation.
• Fixed move-center logic for rotated axes.
• Fixed volume intersection logic.
• Optimized metadata reading during MPR construction.
• The current view will also move when MPR is orthogonal — #769
• Segmentation overlay in MPR — DICOM SEG masks (BINARY / FRACTIONAL / LABELMAP) are now resliced to follow the active MPR planes via SegVolumeBuilder and a dedicated MprController, so the same SEG shown on the source slice appears correctly on coronal, sagittal and oblique reconstructions.

UI / UX

• Toolbar layout and DICOM Explorer layout improved (better spacing, alignment).
• Fixed split series selection behavior in multi-view.
• Improved the info layer display (corner annotations).
• Fixed print layout rendering according to the layout change. Still has some issues to be resolved #509.
• Refactored viewer initialization to use ViewerOpenOptions and enhanced split layout handling.

Networking

• HTTP downloads now exclusively use HttpClient (removed legacy HttpURLConnection paths). Improves how images/series are downloaded.
• Implemented JavaNetHttpClient for OAuth2 authentication flows.
• Refactored org.weasis.core.api.net package; added URIUtils.
• Fixed local file URI exception with HttpClient.

Code & Build Quality

• Updated to Java 25 (both compilation and runtime target).
• Refactored org.weasis.core.api.image and org.weasis.core.api.net packages.
• Replaced File with Path throughout for modern I/O usage.
• Updated to latest weasis-dicom-tools API (5.34.2).
• Fixed bnd-maven-plugin (OSGi bundle generation) compatibility issue.
• Fixed large properties-file loading issue.
• Updated FlatLaf to 3.7.1.

Date/Time Picker

• Replaced the legacy date picker with a new custom DateTimePicker component featuring improved selection UX

SpinnerProgress

• Added a new SpinnerProgress component for displaying indeterminate progress with a spinner animation, used in various loading contexts.

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🐛 Bug Fixes

Commit	Description
f867c06	Redesign tab opening preferences for studies — #806
ee8c27b	Fix very slow initialization of language settings
52618d2	Fix minor display in MPR/MIP/VR
86bf1d3	Fix local file URI exception with HttpClient
bda67cc	Fix preferences initialization in certain launch contexts
77e7dbb	Fix store channel value in volume data
95190bf	Fix MPR geometry
0cc0790	Fix print layout
a6522d4	Fix horizontal banding/striations in MPR COR/SAG views — #771
d1f99e0	Fix deformed axial image in non-axially scanned volumes — #752
6e74788	Fix Optional type handling
2f7e43a	Fix params copy
0952bad	Fix large properties files
2cf44a1	Fix message issue
d522508	Fix wrong class call
dad5ed0	Fix orientation issue
6510528	Fix DICOM presets not loaded for Breast Tomosynthesis — #709
48b54a8	Fix icon transparency

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🧪 Areas to Test for v4.7.0

1. Volume Rendering on macOS (OpenGL 3.3 FBO pipeline) — #784
   • On macOS (Apple Silicon and Intel) verify the VR view opens without GLException and that the volume renders identically to Linux/Windows compute-shader output (same preset, same camera).
   • Force the FBO path on Linux/Windows with -Dweasis.3d.force.fbo=true and compare the result to the default compute-shader output — diffs should be limited to floating-point rounding, not visible artifacts.
   • Resize the VR window and the application window: the FBO texture must be reallocated correctly (no black borders, no stretched output, no GL error in the log).
   • Switch presets (MIP, MinIP, average, composite) and toggle the segmentation overlay to confirm the weighted-splatting accumulators behave correctly on both pipelines.
2. MPR quality — Load several CT/MR volumes including:

   • a regular axial CT,

   • a CT with gantry tilt,

   • an oblique acquisition,

   • a non-axially scanned MR (sagittal-acquired) — #752,

   • a thick-slab CT prone to horizontal banding/striations in the COR/SAG views — #771.

     For each volume, scroll all three planes, take a measurement (length & angle) on axial then on coronal/sagittal, and verify the values are consistent. No banding/striations, no deformation, no geometry mismatch with the source slice.

3. Hanging Protocols groundwork (container layout) — Open studies in the existing layouts (1×1, 2×1, 1×2, 2×2, 3×3, plus the explorer-driven layouts) and confirm:
   • no regression in the way series are placed in the views,
   • no regression in the split series behavior when several series are dropped onto the container,
   • the new ViewerOpenOptions path is used for both local and remote opens.
4. DICOM import — Unified Local Device dialog — #793
   • Drag-and-drop a single DICOM file, a folder, and a .zip containing DICOMs onto the main window — all three should land in the same Local Device dialog.
   • Same three sources via the dialog itself (folder picker / file picker / typing the path).
   • DICOM-ZIP with a password — verify the password prompt appears and the series loads.
   • A nested ZIP (ZIP-of-ZIPs) and a malformed/empty ZIP — verify graceful error handling, no orphan loading panels left behind.
5. Export annotations — On a CT slice with several measurements (length, ellipse, polygon, angle, text annotation):
   • export to each supported format and reopen the result in an external viewer; confirm the geometry, units (px / mm) and labels are preserved,
   • re-import the exported file into Weasis and check round-trip fidelity.
6. 4D sub-series splitting — #763, see also #739
   • Open a multi-phase 4D series (cardiac CT, perfusion MR, dynamic contrast); open the split dialog and verify the suggested phase count matches the source.
   • After splitting, each phase sub-series must be openable in MPR, MIP and VR independently (no cross-phase blending).
7. OAuth2 networking — Configure a WADO-RS/DICOMweb endpoint backed by an OAuth2 IdP (Keycloak or equivalent):

   • first connection triggers the OAuth login; token is cached,

   • token refresh works after expiry without user intervention,

   • revoking the token server-side surfaces a clear error in the UI.

     Verify both the new JavaNetHttpClient path and confirm the legacy code path is no longer reachable (search for HttpURLConnection usage in DICOMweb queries).

8. HTTP(S) downloads on the new HttpClient-only path — Test:
   • HTTP and HTTPS WADO-URI downloads,
   • large series (>500 MB) — verify no memory bloat, progress bar advances,
   • server returning a redirect (302) — followed correctly,
   • local file:// URIs (regression covered by commit 86bf1d3) — must not throw,
   • cancellation mid-download — partial files cleaned up.
9. Print layout
   • Print a 2×2 layout and a 3×3 layout to PDF and to a real printer; verify scaling, aspect ratio, info-layer rendering and that no view is clipped.
   • #509 is not yet fixed. So we need to ckeck there is no regression from the previous version.
10. Preferences initialization — Cover the cold-start and re-launch scenarios that previously threw NPE during UICore initialization (commit bda67cc):
    • first launch on a clean profile (no ~/.weasis/preferences/),
    • launch with a partially written preferences file (simulate a previous crash),
    • launch with read-only preferences directory,
    • language change followed by restart (regression for commit ee8c27b — "very slow init of language settings").
11. Java 25 compatibility — Run the full matrix:
    • build with JDK 25 (Temurin) and JDK 26 (CI target) — both must pass mvn -B -ntp verify -Pcoverage,
    • launch the packaged application on Windows / macOS (Intel & Apple Silicon) / Linux,
    • run the installer pipeline (build-installer.yml via workflow_dispatch) — MSI / PKG (notarized) / DEB / RPM all produced and installable,
    • verify all GitHub Actions jobs use JDK 25/26 (no leftover JDK 21 references).
12. weasis-dicom-tools 5.34.2 upgrade — Major refactor of image conversion and DICOM tooling. Test:
    • DICOM import of CT, MR, US, XA, MG, NM, PT, RT (plan/struct/dose), SR, KO,
    • DICOM export of single image, full series, and a multi-frame object,
    • transcoding between encapsulated transfer syntaxes (JPEG-Lossless, JPEG2000, RLE, HTJ2K when supported),
    • DICOMweb: WADO-RS retrieve, STOW-RS send,
    • DIMSE: C-STORE, C-FIND, C-MOVE, C-GET against a known SCP (dcm4chee or equivalent),
    • image processing pipeline: windowing, VOI/Modality LUT, palette color, MONOCHROME1 inversion, PR application, KO filter — verify pixel-perfect equivalence with v4.6.6 on a reference dataset.
13. MIP projection in the 2D viewer — #795
    • Activate MIP on a CTA volume; verify the slab geometry overlay (thickness handles, orientation indicator) is drawn,
    • change slab thickness with the mouse and with the keyboard; the projection updates in real time,
    • synchronize the MIP view with a sibling 2D view (same FoR) — scroll & W/L propagate as expected,
    • switch between MIP / MinIP / Average and verify the projection mode label updates in the info layer.
14. DICOM export from MPR — #796
    • Export an axial, coronal, sagittal and oblique MPR; reopen each exported series in Weasis and in an external viewer,
    • verify ImageOrientationPatient / ImagePositionPatient reflect the chosen plane,
    • export with and without burned-in annotations and confirm both behave correctly,
    • check the exported series appears under the correct study in the DICOM Explorer.
15. MPR crosshair cut mode in VR — #799
    • With an MPR + VR layout, enable the crosshair cut mode on the VR view,
    • drag the MPR crosshairs and verify the clipping planes update in real time on the volume,
    • toggle individual axis cuts on/off — the volume must reveal/hide the corresponding half-space,
    • reset the crosshair to volume center — clipping planes must reset accordingly.
16. System native file chooser — #761
    • On Windows, macOS and Linux (GTK), open every "Open"/"Save" dialog reachable from the UI (DICOM import, export annotations, screenshot, preferences import/export…) and verify the OS-native picker is shown (not the Java Swing one),
    • verify common shortcuts (recent files, drives/volumes, hidden files toggle on macOS) work,
    • verify the dialog respects the file-type filters declared by the caller.
17. Customizable keyboard shortcuts — #804
    • Open the new Shortcuts preferences panel; verify all actions are listed and searchable,
    • rebind a shortcut to a new key, restart the application, confirm the new binding is persisted,
    • try to bind two actions to the same chord — conflict detection must warn,
    • export the shortcut configuration, reset to defaults, then re-import — bindings must be restored,
    • verify the rebound shortcuts actually trigger their actions in the viewer.
18. Tab opening preferences for studies — #806
    • Test the four import contexts: local + new study, local + same study, network + new study, network + same study,
    • verify TabFocusPolicy.autoByDuration behaves consistently across these contexts (focus follows the most recent open within the configured time window),
    • exercise the redesigned preferences dialog — every option must be persisted across a restart and reflected in the runtime behavior.
19. DICOM Segmentation (BINARY / FRACTIONAL / LABELMAP) in 2D, MPR and 3D
    • Open a series with a BINARY SEG attached; verify each segment is selectable in the Segmentation tool, the contour overlay matches the source slice, and turning a segment off hides it in 2D, MPR and VR simultaneously.
    • Open a series with a FRACTIONAL SEG (PROBABILITY and OCCUPANCY when available); verify the alpha LUT renders intermediate values (not a hard 0/1 mask) and that the per-segment opacity slider in the Segmentation tool affects the blend.
    • Open a series with a LABELMAP SEG; verify all segment labels are picked up from the single per-slice frame and that segment numbering matches the source SegmentSequence.
    • Build an MPR from a series carrying a SEG; scroll/rotate the planes and verify the overlay tracks the reformatted geometry on axial, coronal, sagittal and oblique cuts (no offset, no aliasing on borders).
    • Open the same SEG in the 3D Volume Rendering view; verify the overlay is visible inside the volume, that the per-segment color/visibility toggles in the Segmentation tool propagate to VR, and that the SegVolumeTexture upload does not regress 3D performance.
    • Load an RT Dose with isodose levels; verify it now renders through the fractional-overlay path and looks visually equivalent to v4.6.6.
20. View synchronization overhaul — exercise every entry point and verify the new defaults:
    • Open a CT/PET pair sharing a FoR; confirm only Scroll propagates by default; toggle Window/Level and Zoom in the per-view popup and verify propagation; use Apply to all synchronized views and check that the per-view version stays inside the FoR group while the toolbar drop-down version applies to every sync-active view in the container.
    • Open three or more series with different FoRs in the same container; verify each auto-sync button shows a distinct color chip in its center, and that swapping the layout keeps each FoR's color stable. Containers with a single FoR must show no chip.
    • Manual sync: open two same-orientation series with no shared FoR; click the hand button and verify auto-link with a single candidate, the multi-select picker with multiple candidates, and the auto-join behaviour when joining an existing manual group. Confirm Scroll is forced on and locked.
    • MPR: open a volume in the MPR viewer and verify the {{< icon viewSettings >}} settings popup contains a Synchronize submenu without a master toggle, with the same per-action toggles + Apply to all synchronized views + Close.
    • Toolbar drop-down: confirm the None mode is gone and the master Synchronize checkbox correctly enables/disables synchronization globally without changing the active mode.